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Releases: tolkit/gfatk

Bellonia

10 Jul 09:56
@Euphrasiologist Euphrasiologist
0.2.2
b6e4771
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Bellonia Latest
Latest

Hopefully last release with gfatk linear fixes. This one fixes an annoying bug where the orientations of the segments were not correct in some cases. Full changelog below.

  • Merge pull request #11 from tolkit/fix-linear Sat, 9 Jul 2022 21:05:26 +0100
  • Finally fixed linear Sat, 9 Jul 2022 21:00:03 +0100
  • Remove printing debugging info. Tue, 5 Jul 2022 17:09:12 +0200
  • Small change to logic. Tue, 5 Jul 2022 11:57:18 +0200
  • Add prototype fix to be tested for gfatk linear. Increase version number too. Tue, 5 Jul 2022 11:27:51 +0200
  • Bug fix in linear when wrong path orientations sometimes used. Mon, 4 Jul 2022 17:02:07 +0200
  • Version update Fri, 1 Jul 2022 13:25:49 +0100
  • Fix gfatk path, where path only a single segment. Fri, 1 Jul 2022 11:08:42 +0100
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Tribounia

28 Jun 14:36
@Euphrasiologist Euphrasiologist
0.2.16
36f52a9
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Tribounia

Minor things, most notably preventing stack overflows from happening by placing a recursion limit on the gfatk linear functionality. Other minor changes below:

  • Update docs. Tue, 28 Jun 2022 15:27:58 +0100
  • Update to v0.2.16. Tue, 28 Jun 2022 15:27:28 +0100
  • Print recursion information and depth. Tue, 28 Jun 2022 15:27:05 +0100
  • Make error in gfatk path more readable. Tue, 28 Jun 2022 15:24:12 +0100
  • Get the version right. Tue, 28 Jun 2022 15:22:44 +0100
  • Update examples for tutorial. Tue, 28 Jun 2022 15:21:34 +0100
  • Fixes #9. Fall back on normal linearisation if recursion limit exceeded. Tue, 21 Jun 2022 16:40:45 +0100
  • Update examples. Thu, 16 Jun 2022 16:21:04 +0100
  • Edit version number on README.md page. Thu, 16 Jun 2022 15:33:10 +0100
  • Edit examples dir. Update README.md. Thu, 16 Jun 2022 15:31:22 +0100
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Cecropia

16 Jun 14:24
@Euphrasiologist Euphrasiologist
0.2.14
349f499
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Cecropia

Important update. A few bugs ironed out in gfatk linear. Support tabular output in gfatk stats. See full log below.

  • Better error handling on gfatk extract if input node not found. Thu, 16 Jun 2022 09:14:31 +0100
  • Paths of length 2 now dealt with in gfatk linear. Wed, 15 Jun 2022 21:44:49 +0100
  • Version bump for release. Wed, 15 Jun 2022 17:34:50 +0100
  • Bug: gfatk linear fix when evaluating multiple subgraphs. Wed, 15 Jun 2022 17:22:19 +0100
  • Minor version release. Wed, 15 Jun 2022 12:27:32 +0100
  • Fixes #7. Add node threshold to linear. Wed, 15 Jun 2022 11:34:44 +0100
  • Update docs. Tue, 14 Jun 2022 08:23:13 +0100
  • Tabular output support for gfatk stats. Tue, 14 Jun 2022 08:22:49 +0100
  • Update docs. Mon, 13 Jun 2022 09:52:45 +0100
  • Add whether a subgraph is cyclic or not to the output header of gfatk linear . Mon, 13 Jun 2022 09:50:53 +0100
  • Update docs accordingly. Fri, 10 Jun 2022 21:58:27 +0100
  • Making clippy happier. Fri, 10 Jun 2022 21:56:11 +0100
  • Edits to stats. Mito/chloro should output multiple subgraphs matching the criteria. Fri, 10 Jun 2022 15:26:42 +0100
  • Linked gfatk linear fasta headers to the subgraph they come from. Thu, 9 Jun 2022 20:28:26 +0100
  • Single nodes with the -e flag in gfatk linear are now emitted. Thu, 9 Jun 2022 17:24:41 +0100
  • Added info to Cargo.toml for crates.io publish. Mon, 6 Jun 2022 19:58:03 +0100
  • Update README.md curl links. Wed, 1 Jun 2022 15:11:28 +0100
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Hatiora

01 Jun 14:10
@Euphrasiologist Euphrasiologist
0.2.0
fe16c62
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Hatiora

Mainly added unit testing, and documentation. Other additions are relatively minor bugs. Full log below.

  • Make exit more rusty. Wed, 1 Jun 2022 14:56:26 +0100
  • Fix bug of single segment in linear. Wed, 1 Jun 2022 14:52:13 +0100
  • Update documentation. Fri, 27 May 2022 11:31:04 +0100
  • Update documentation in README.md. Fri, 27 May 2022 11:19:15 +0100
  • Fixes #5. gfatk extract takes more than one segment ID. Thu, 26 May 2022 21:26:34 +0100
  • Same API to extract-mito. Tue, 10 May 2022 11:30:50 +0100
  • More sensible limits to gfatk extract-chloro GC% Mon, 9 May 2022 16:07:39 +0100
  • Remove thiserror dependency. Mon, 9 May 2022 12:19:42 +0100
  • Closes #3 but now in new subcommand. Closes #4. Mon, 9 May 2022 10:05:00 +0100
  • Fixes #1. Linear operates within subgraphs too with a flag. Thu, 28 Apr 2022 16:14:10 +0100
  • Update docs. Sun, 24 Apr 2022 18:07:23 +0100
  • Add ./src/gfa.rs tests. Sun, 24 Apr 2022 17:40:42 +0100
  • Update docs. Sat, 23 Apr 2022 11:34:20 +0100
  • Graph tests added. Sat, 23 Apr 2022 11:33:37 +0100
  • Adding more tests. Fri, 22 Apr 2022 17:04:44 +0100
  • Arrow to comma in fasta header. Tue, 29 Mar 2022 15:55:33 +0100
  • Remove spaces from the fasta header. Fri, 25 Mar 2022 17:48:16 +0000
  • Typo in fasta header Fri, 25 Mar 2022 16:49:43 +0000
  • Remove .DS_Store again... Fri, 25 Mar 2022 16:43:49 +0000
  • Add path info to the linearised fasta header. Fri, 25 Mar 2022 16:43:24 +0000
  • Update README.md Tue, 15 Mar 2022 12:18:33 +0000
  • Remove .DS_Store Tue, 15 Mar 2022 10:56:48 +0000
  • Add unit testing. Remove a couple bugs. Tue, 15 Mar 2022 10:55:44 +0000
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gfatk 0.1.4

15 Mar 12:18
@Euphrasiologist Euphrasiologist
0.1.4
642bb53
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gfatk 0.1.4

Testing added, and a few bugs removed.

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gfatk 0.1.3

14 Mar 11:57
@Euphrasiologist Euphrasiologist
0.1.3
fd3e1b4
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gfatk 0.1.3

First release of the gfatk tool. Available on Mac & Linux (ubuntu).

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